Question: When using MACS2 with -f BAM, it is possible to have a shift other than 0?
gravatar for Lucy
10 months ago by
Lucy0 wrote:


In the manual for MACS2, there is the following statement in the information about the --shift option: "Note, you can't set values other than 0 if format is BAMPE or BEDPE for paired-end data. Default is 0"

Is this also the case if the format is set as BAM or can I have different shift sizes with BAM? The command I would like to use to analyse my ATAC-seq data is as follows:

macs2 callpeak <input file> -f BAM --no-model --shift -100 --extsize 200 --keep-dup-all --call-summits

Many thanks, Lucy

macs2 macs • 346 views
ADD COMMENTlink modified 9 months ago by Biostar ♦♦ 20 • written 10 months ago by Lucy0

My understanding is that you do not need any shifting parameters when using --nomodel. Is this ATAC-seq?

ADD REPLYlink written 10 months ago by ATpoint19k

Yes this is ATAC-seq data.

ADD REPLYlink written 10 months ago by Lucy0

Did you solve your problem or do you need further assistance? You raised this question in different posts, that is why I am asking.

ADD REPLYlink modified 9 months ago • written 9 months ago by ATpoint19k

Thanks for the message. I think I have decided to go with -f BAMPE and no shifting.

ADD REPLYlink written 9 months ago by Lucy0
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